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© 1995 Oxford University Press 575-582

Footnote

Sequence-independent inhibition of RNA transcription by DNA dumbbells and other decoys

Sequence-independent inhibition of RNA transcription by DNA dumbbells and other decoys Carol S. Lim* , Nabila Jabrane-Ferrat 1 , Joseph D. Fontes 1 , Hiroshi Okamoto 1 , Marvin R. Garovoy 2 , B. Matija Peterlin 1 and C. Anthony Hunt

Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-0446, USA, 1 Departments of Medicine, Microbiology and Immunology, Howard Hughes Medical Institute, University of California-San Francisco and 2 Department of Surgery, School of Medicine, University of California-San Francisco, San Francisco, CA, USA

Received October 3, 1996; Revised and Accepted November 23, 1996

ABSTRACT

DNA dumbbells are stable, short segments of double-stranded DNA with closed nucleotide loops on each end, conferring resistance to exonucleases. Dumbbells may be designed to interact with transcription factors in a sequence-specific manner. The internal based paired sequence of DNA dumbbells in this study contains the X-box, a positive regulatory motif found in all MHC class II DRA promoters. In electrophoretic mobility shift assays (EMSAs), dumbbells and other oligonucleotides (`decoys') with the core X-box sequence were found to compete with the native strand for binding to X-box binding proteins (including RFX1). However, only the X-box dumbbell was capable of forming detectable complexes with such proteins using EMSA. In a model cell system, dumbbells were tested for their ability to block RFX1VP16 activation of a plasmid containing multiple repeats of the X-box linked to the CAT gene. While it appeared that dumbbells could block this activation, the effect was non-specific. This and further evidence suggests an inhibition of transcription, most likely via an interaction with the general transcriptional machinery.

INTRODUCTION

Selective regulation of gene expression is a direct way to treat major diseases such as cancer, viral infections and various genetic disorders. While there are numerous reports on strategies targeting mRNA via antisense oligonucleotides ( 1 ) and DNA via triplex formation ( 2 ), targeting the proteins which regulate expression of a specific gene is a relatively novel approach. These `gene regulating' proteins are transcription factors (TFs) which bind to DNA in a sequence-specific manner. There have been several reported cases of utilizing sequence-specific DNA decoys for selective sequestering of TFs, rendering them unavailable to bind to their target DNA on the gene ( 3 - 5 ). The final result is a blockade of transcriptional activation.

Several different forms of double-stranded DNA have been utilized as decoys for TFs, including unmodified oligonucleotide duplexes ( 6 ), [alpha][beta]-anomeric (chirally modified) oligonucleotides ( 7 ), phosphorothioate oligonucleotide duplexes ( 3 ) and dumbbell DNA ( 5 ). Use of phosphorothioate oligonucleotide duplexes may overcome the inherent disadvantage of nuclease susceptibility that is typical of unmodified oligonucleotides. However, recent studies have shown that double-stranded phosphorothioate oligonucleotides may exhibit sequence-independent effects due to non-specific protein binding ( 8 ). Chirally modified oligonucleotides are also nuclease resistant, but they require special synthesis techniques. It is also unclear which chiral form(s) will be recognized by a given TF, if at all.

Dumbbell DNA, on the other hand, has increased stability to exonucleases ( 9 ), is easy to synthesize, cannot undergo strand separation and has a non-toxic unmodified backbone which resembles natural DNA. These characteristics make dumbbell DNA an excellent candidate for TF binding and competition studies. While dumbbell DNA has been extensively studied as a physical model for various DNA conformations ( 10 - 12 ), little is known about its biological relevance, i.e. if dumbbell DNA will even be recognized by its target TF. On a rudimentary level, if dumbbell DNA has a specified DNA recognition sequence, it should. However, compared to a long, typical duplex segment of DNA, dumbbell DNA might adopt a different, abiotic conformation. Additionally, the TF itself may require flanking sequences or other factors for binding in addition to the specific DNA recognition sequence.

Dumbbells with a loop composition of all thymidines (Ts) and a loop size of 4 nt were chosen for our initial studies based on several DNA hairpin studies. Blommers et al . ( 13 ) showed that a particular DNA hairpin was maximally stable when the loop was comprised of 4 (or 5) nt. Additionally, Senior ( 14 ) found that for their specific hairpin, homonucleotide loops were the most stable. Additional experiments utilized all A loop dumbbells and highly stable CTTG loop dumbbells.

The internal duplex sequence of DNA dumbbells and other double-stranded oligonucleotides were designed to mimic the X-box of the DRA promoter, essential in regulating expression of the Major Histocompatibility Complex (MHC) class II gene. The X-box is a positive regulatory motif conserved in all MHC class II promoters. Several TFs appear to target that sequence, including the RFX (Regulatory Factor X) family of TFs (for a review see 15 ).

In in vitro binding assays, the X-box dumbbell was found to interact with at least one of the RFX family members, RFX1. To verify these results in vivo , a reporter gene assay was devised to elucidate whether dumbbells could block RFX1 activity. A plasmid containing the cDNA of RFX1 fused to the transcriptional activation domain of adenovirus VP16 was constructed (pRFX1VP16). The product of this plasmid can bind to and activate p4XBCAT, which contains four repeats of the X-box linked to the CAT gene. The initial results of this assay showed that oligonucleotides with the core X-box sequence were able to block RFX1 activation. Surprisingly, ligated dumbbells were no more active than unligated oligonucleotides. However, control oligonucleotides were also active and transcription of unrelated reporter gene systems was also reduced. Oligonucleotides had no effect on transfection efficiency of plasmids based on a PCR assay. However, an RNase protection assay indicated that active oligonucleotides decreased mRNA levels, suggesting an effect on polymerase II or its associated transcriptional machinery.

MATERIALS AND METHODS

Oligonucleotidenucleotide sequences

Oligonnucleotides were obtained from either Keystone Laboratories (Menlo Park, CA) or Oligos Etc. (Wilsonville, OR). Control oligonucleotides contain irrelevant sequences. Oligonucleotide sequences and nomenclature are listed in Table 1 . `Core X-box oligonucleotides' refers to all oligonucleotides with the X-box internal sequence (these include all oligonucleotides listed in Table 1 except for the `ctrl' oligonucleotides).


Table 1 . Oligonucleotide and dumbbell DNA nomenclature and sequences (complementary sequences are underlined where it is not apparent)

Synthesis of dumbbell DNA

An intramolecularly annealing (i.e. self-complementary) oligonucleotide was phosphorylated (with T4 polynucleotide kinase) then ligated (with T4 DNA ligase) to form dumbbell DNA as described elsewhere ( 16 ). For radiolabeled oligonucleotides/dumbbells ( 32 P phosphorylation) in a 10 [mu]l volume, 10 pmol oligonucleotide was incubated with 1 U T4 polynucleotide kinase (US Biochemical), 20 [mu]Ci [[gamma]- 32 P]ATP (Amersham), 50 mM Tris-HCl, pH 7.6, 10 mM MgCl 2 and 10 mM 2-mercaptoethanol at 37oC for 1 h. Ligated refers to dumbbell products and unligated (unl) refers to the starting reactant oligonucleotide. For ligation of 32 P-labeled oligonucleotides, 5 pmol 32 P-labeled oligonucleotide was ligated in a 10 [mu]l volume with 1 U T4 DNA ligase, 5% polyethylene glycol, 66 mM Tris-HCl, pH 7.6, 6.6 mM MgCl 2 , 10 mM DTT and 66 [mu]M ATP at 16oC for 48 h.

Purification

Dumbbells were purified on 12% denaturing (8.5 M urea) polyacrylamide gels ( 17 ). The ligation reaction mixtures were visualized by UV shadowing and products (dumbbells) were isolated by slicing and removing the appropriate bands. Products were eluted from gel slices for 30 min using the BioRad Model 422 electroeluter, ethanol precipitated and purified on NAP-5 (Sephadex G-25) columns (Pharmacia LKB, Uppsala, Sweden) using 1 mM Tris-HCl, 0.1 mM EDTA, pH 7.6. Radiolabeled oligonucleotides/dumbbells were similarly gel purified (but not electroeluted). Gel slices from these reactions were instead eluted overnight with 100 [mu]l TE (10 mM Tris-HCl, 1 mM ETDA, pH 7.6) at room temperature. Unligated oligonucleotides were purified by HPLC by the manufacturer and used directly.

Proof of ligation (nuclease/phosphatase reactions and restriction enzyme cleavage)

Proof of ligation experiments have been described elsewhere ( 16 ) and are summarized as follows. The product (dumbbell DNA) was subjected to three enzymes: the Klenow fragment of Escherichia coli , S1 nuclease and shrimp alkaline phosphatase. In all three cases, dumbbell DNA was more resistant to degradation compared with its corresponding unligated sequence. The restriction enzyme Mae I was used to show that the dumbbell DNA formed a cleavable, recognizable duplex.

Cell culture, nuclear extracts, antibody ( [alpha] RFX1)

Class II-expressing Raji cells (an EBV-positive human Burkitt's lymphoma B cell line) were grown in RPMI 1640 medium with 10% fetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 [mu]g/ml) and L-glutamine (292 [mu]g/ml). Cos7 cells, a SV40-transformed monkey kidney cell line, were grown in Dulbecco's modified Eagle's medium (with 4.5 g/l glucose) and FBS and antibiotics as above. Nuclear extracts were prepared from Raji cells as described previously ( 18 ), except that the supernatant was not diluted in the last step. [alpha]RFX1 (anti-RFX1 antibody), which recognizes the N-terminus of recombinant RFX1, was prepared as previously described ( 19 ).

Electrophoretic mobility shift assays (EMSAs)

Competition assay. Nuclear extract containing RFX1 was incubated with radiolabeled DRAX and various unlabeled competitors. The X dumbbell, unl X, ctrl dumbbell 1, unl ctrl 1, ds X, ds S-X or ns 10 was used as competitor at 150-fold excess over radiolabeled DRAX. Specifically, the binding assay at 0oC included 10 [mu]g nuclear extract and 10 pmol unlabeled competitor in the binding buffer described by Reith ( 20 ) with 1-2 [mu]g poly(dI[middot]dC)[middot]poly(dI[middot]dC) incubated for 10 min, followed by the addition of 32 P-labeled DRAX probe (0.066 pmol or 12 000 c.p.m.) for an additional 20 min. For this and the following EMSA gels, samples were loaded onto 5% native polyacrylamide gels and run with recirculating 0.25* TBE buffer for 2-3 h at 10 mA and 150 V at room temperature. After drying, gels were exposed to X-ray film for 1-3 days at -70oC. RFX1 supershift with antibody. Nuclear extract was incubated with either 2 [mu]l [alpha]RFX1 or 10 pmol unlabeled competitor oligonucleotide (DRAX or X-box dumbbell) under the conditions described above, with the addition of 50 ng E.coli DNA and 0.1% Nonidet P-40 at the start of incubation. After 10 min, radiolabeled DRAX was added and the mixture was incubated for an additional 20 min.

Direct binding assay

Nuclear extract was incubated with radiolabeled oligonucleotides/ dumbbells (0.066 pmol or 15 000 c.p.m.) for 20 min at 0oC under the conditions mentioned for the competition assay.

Transfections and reporter gene assays

RFX1 activation of 4XBCAT. Aliquots of 1 * 10 5 Cos7 cells were plated in 6-well plates the day before transfection. Plasmids pRFX1VP16 (2 [mu]g) and p4XBCAT (1 [mu]g) plus 50 nM oligonucleotide were co-transfected with lipofectin (Gibco BRL, Gaithersberg, MD) using the manufacturer's protocol. The concentration of the oligonucleotide in the transfecting medium was four times that of the final oligonucleotide concentration. In other words, for an oligonucleotide with a final concentration of 50 nM, the concentration in the transfecting medium was 200 nM. Transfections were performed at least twice in triplicate. For RNase protection assays, large scale transfections of 5 * 10 5 Cos7 cells in 100 mm plates (2.4 [mu]g pRFX1VP16 and 1.6 [mu]g p4XBCAT, 50 nM oligonucleotides) were performed. Control transfections. In separate transfections, 0.5 [mu]g CMV promoter-driven plasmid pCRtm3-CAT (Invitrogen, San Diego, CA) was used as an expression control plasmid. These control transfections were performed at least twice in duplicate. Another control utilized 2 [mu]g pSV[beta]gal (Promega, Madison, WI), transfected into 2 * 10 5 cells on 60 mm plates (performed twice in triplicate). Both control transfections included various oligonucleotides at 50 nM and were performed on Cos7 cells. Plasmid constructs. pRFX1VP16 was constructed by first amplifying the RFX1 cDNA (a gift of B.Mach) with primers that introduced a Hin dIII site after the final amino acid codon. This cDNA was subcloned into pSVSPORT1 (Life Technologies, Grand Island, NY) and the cDNA coding for the activation domain of VP16 from herpes simplex virus (amino acids 400-479) was ligated into the introduced Hin dIII and Sal I sites of the plasmid. The plasmid p4XBCAT contains four X-box repeats and has been described previously ( 21 ). CAT assays. Cells were harvested for CAT assays ~48 h after electroporation. CAT assays were performed on cell lysates as described previously ( 22 , 23 ). Protein content (A 595 ), determined using the Bradford assay (using BioRad Protein Assay Reagent), was used to normalize CAT activity. In some cases cell counts were also taken to determine viability.

[beta] -Galactosidase assays. Cells were stained in situ for [beta]-galactosidase activity and visually inspected for blue cells. A qualitative result was obtained by removing the cells from the plates with trypsin and counting blue cells.

PCR of transfected DNA

DNA was extracted from cells transfected with 2 [mu]g pRFX1VP16 and 1 [mu]g p4XBCAT with or without oligonucleotide using a modified Hirt assay ( 24 ) with an incubation time and temperature of 1 h and 50oC respectively. Each PCR reaction in a total volume of 100 [mu]l contained 10 [mu]l template DNA, 0.2 mM dNTPs, 100 pmol primers V1/V2 (for pRFX1VP16; V1, GCC ACC ATG GCA TCG ACG GCC CCC CCG ACC GAT; V2, GTC GAC CCC ACC GTC CTC GTC AAT TCC), 1 U Taq DNA polymerase (Boehringer Mannheim), 10 mM Tris-HCl, 50 mM KCl, pH 8.3, and 2.5 mM MgCl 2 . All samples (including controls) were subjected to 25 cycles of amplification (30 s denaturing at 94oC, 30 s annealing at 60oC, 60 s extension at 74oC) and were loaded onto a 1.5% agarose gel (with ethidium bromide) and photographed under UV illumination for analysis.

RNase protection assay

Cells from large scale transfections were harvested as pooled duplicates, 48 h post-transfection. Cytoplasmic RNA was isolated from these cells using the method of Kao et al . ( 25 ) for use in RNase protection assays. The RNA probe was prepared by linearizing pCRtm3-CAT with Pvu II. This created three fragments, one of which was in vitro transcribed by T7 polymerase using the MAXIscripttm system (Ambion, Austin, TX) to generate a 32 P-labeled fragment of 173 nt. This probe was complementary to a 111 nt region of the CAT transcript. In addition, a 32 P-labeled 18S rRNA internal standard probe (116 nt transcript, 80 nt of which are complementary to rRNA from all vertebrates) was prepared using linearized pT7 RNA 18S (Ambion). Protection assays were performed using the Guardian RNase protection assay kit (Clontech, Palo Alto, CA) with hybridization at 42oC overnight. CAT RNA and 18S RNA were probed separately. Samples were heated at 95oC for 5 min before loading onto a 6% denaturing (8 M urea) acrylamide gel and electrophoresed in TBE buffer for 1.5-2 h at 500 V. After drying, gels were exposed to X-ray film overnight at -70oC.

RESULTS

All oligonucleotides/dumbbells with the core X-box sequence were able to compete for binding to X-box binding proteins (RFX1)

In order to determine which oligonucleotides/dumbbells interact with X-box binding proteins, EMSAs were performed. B cell nuclear extracts were first incubated with a radiolabeled 26 bp X-box probe (DRAX) with or without competitor oligonucleotides/ dumbbells. The unlabeled competitors, X dumbbell, unl X, ds X and the ds S-X (Fig. 1 , lanes 3, 4, 7 and 8 respectively) successfully competed with DRAX for binding to X-box binding proteins. As little as a 30-fold excess of unl X was able to compete with DRAX (data not shown). Oligonucleotides with irrelevant sequences were unable to compete for the formation of shifted complexes (Fig. 1 , lanes 5, 6 and 9).

Only the X dumbbell could form a detectable complex with X-box binding proteins (RFX1)


Figure 1 . Competition gel. In all lanes, competitor oligonucleotides were added to 32P-labeled DRAX probe incubated with nuclear extract.

Next, direct binding assays between X-box binding proteins and oligonucleotides/dumbbells were performed. B cell nuclear extracts were incubated with radiolabeled oligonucleotides/dumbbells. Only the ligated X-box dumbbell (X dumbbell) was capable of forming a detectable shifted complex (Fig. 2 A, lane 4) using this technique. Other oligonucleotides, including ds X, unl X, ctrl dumbbell 1 and unl ctrl 1 could not form detectable complexes with X-box binding proteins (Fig. 2 A, lanes 3 and 5-7 respectively) under these conditions. Because we were unable to efficiently label the phosphorothioate oligonucleotide (ds S-X) with 32 P, it could not be used to determine whether it could bind to any of the X-box proteins. Others ( 8 ) have reported similar problems with kinase labeling of phosphorothioate oligonucleotides, which could be due to the inhibitory effect of some phosphorothioate oligonucleotides on T4 polynucleotide kinase ( 26 ).


Figure 2 . (A) Direct binding gel. 32 P-Labeled oligonucleotides (listed above the gel) were tested for their ability to directly bind to RFX. (B) Supershift. All lanes contain 32 P-labeled DRAX, with various competitors (listed above gel). Lane 1, RFX binding to DRAX, indicated by bands a and b; lane 3, [alpha]RFX1 supershifting of band a; lane 4, X dumbbell competes off both bands a and b.

RFX1 is one of the X-box binding proteins that interacts with dumbbell DNA

To ascertain if RFX1 interacts with dumbbell DNA, a supershift assay was utilized. Inclusion of [alpha]RFX1 in the EMSA binding reaction resulted in a decrease in the electrophoretic mobility of the complex, indicating that it contained RFX1 (Fig. 2 B, lane 1, a). The X dumbbell was able to compete for and (weakly) bind to the RFX1-containing complex and the lower unidentified complex as well (Fig. 2 b, lane 4, b). This lower band is most likely another member of the RFX family ( 27 , 28 ).

Ligated/unligated dumbbells of any sequence and the phosphorothioate oligonucleotide (ds S-X) were able to block RFX1VP16 activation of p4XBCAT

Since core X-box oligonucleotides/dumbbells were able to interact with RFX1 in vitro , the next step was to determine if these oligonucleotides/dumbbells could specifically inhibit transcriptional activation by RFX1 in vivo . The plasmid pRFX1VP16 expresses a protein consisting of RFX1 fused to the strong VP16 transcriptional activating domain of herpes simplex virus. This fusion protein is a potent transcriptional activator dependent only on RFX1 binding to its target sequence. The p4XBCAT plasmid contains multiple repeats of the X-box, the target for RFX1, which allows for strong transactivation. Dumbbells, unligated oligonucleotides, double-stranded oligonucleotides and double-stranded phosphorothioate oligonucleotides were tested for their ability to block RFX1VP16 activation of p4XBCAT. Initial studies indicated that optimal (e.g. maximal effect with no toxicity) oligonucleotide concentrations in Cos7 cells were in the range 50-100 nM (data not shown). The phosphorothioate oligonucleotide (ds S-X) at 50 nM always had higher or similar cell counts (viability) compared with no oligonucleotide added (data not shown).

Since the ligated dumbbell (X dumbbell) was the only oligonucleotide capable of forming a detectable complex with RFX1 (under the conditions of these EMSAs), it was anticipated that they would be the most potent inhibitors of RFX1VP16 activation of 4XBCAT. Clusel et al. showed that ligated (but not unligated) dumbbells specific for the transcription factor HNF-1 were able to block HNF-1 activation of a CAT reporter plasmid ( 5 ). In our system, however, it was found that ligated dumbbells were no more active than unligated in blocking RFX1VP16 activation of p4XBCAT (data not shown). Thus, the activity of oligonucleotides in this system is not dependent on a ligated, double-stranded structure.

As seen in Figure 3 , core X-box oligonucleotides, including unl X and ds S-X, were effective in down-regulating CAT activity. ds X was much less active, presumably due to degradation by exonucleases. A hairpin X-box (loop on one end only) was of intermediate activity. Cell viabilities were relatively stable among all samples. Significantly, control (irrelevant) sequence unligated oligonucleotides (unl ctrl 2 and unl ctrl 3) inhibited RFX1VP16 activation of 4XBCAT. The activity of these irrelevant oligonucleotides suggested a non-specific effect of unligated oligonucleotides in general on the function of RFX1VP16. Another double-stranded phosphorothioate (with the same internal sequence as unl ctrl 3) was also able to decrease RFX1VP16 activation of 4XBCAT to the same extent as ds S-X (data not shown).


Figure 3 . RFX1VP16 activation of 4XBCAT. Cos7 cells were transfected with pRFX1VP16 and p4XBCAT, along with 50 nM oligonucleotide treatments as above. The activity of these oligonucleotides is reflected in their ability to down-regulate CAT activity (shown by black bars). Cell counts are indicated by white bars. Experiments were performed at least twice in triplicate (error bars indicate +- 1 SD).

To investigate if the loop structure of these unligated oligonucleotides could influence activity, two other unligated X-box oligonucleotides (in addition to the T loop) were tested. The first contains CTTG loops (unl CTTG-X-box), the second contains A loops (unl A-X), both in place of T loops. Unl CTTG-X contains the highly thermodynamically stable G(CTTG)C loop ( 11 , 29 ) on each end instead. Unl A-X should be the least stable of these three based on DNA hairpin studies ( 14 ). Both of these oligonucleotides were active as well; the CTTG loop oligonucleotide (unl CTTG-X) was slightly more active than or similarly active as the T loop oligonucleotide (unl X); the A loop oligonucleotide (unl A-X) was the least active of the three.

Active oligonucleotides/dumbbells were able to decrease reporter gene readouts in two other systems as well

As control experiments, some of the core X-box oligonucleotides at 50 nM were tested for their effect on other reporter gene systems, including CMVCAT and SV[beta]gal, neither of which were expected to be specifically regulated by any of the core X-box oligonucleotides. CMVCAT transfection results are shown in Figure 4 . Reduction of reporter gene readout by various oligonucleotides in this system followed the same trend as that of the RFXVP16/4XBCAT system.


Figure 4 . CMVCAT control. Cos7 cells were transfected with pCMVCAT (a control plasmid) along with 50 nM oligonucleotide treatments as above. Activity of oligonucleotides is measured by ability to decrease CAT activity (as in Fig. 3). CAT activity (%) is listed to the right of each bar. Experiments were performed at least twice in duplicate.

Active oligonucleotides could possibly interact with the CAT gene itself (or some aspect of the assay), therefore, an entirely different reporter gene/assay was tested. The pSV[beta]gal reporter gene consists of SV40 promoter/enhancer sequences which drive the lacZ gene, encoding the [beta]-galactosidase ([beta]-gal) enzyme. Production of [beta]-gal can be detected by the appearance of a blue color when mixed with substrate ( 30 ). For SV[beta]gal assays, only the two most potent oligonucleotides were tested (ds S-X and unl CTTG-X). Compared with SV[beta]gal alone, ds S-X-treated cells expressed only 2-3% cells which stained blue, while unl CTTG-X-treated-cells expressed ~20% blue cells. The same non- specific effect was mirrored with these two reporter genes as well, i.e. in terms of activity, ds S-X > unl CTTG-X > unl X > ds X.

Active oligonucleotides/plasmids did not alter transfection efficiency/uptake of reporter plasmids

The non-specific inhibition of transcription may have been due to the oligonucleotides/dumbbells ability to reduce transfection efficiency. To address this issue, Cos7 cells transfected with plasmids in the presence or absence of oligonucleotide were harvested, lysed and the plasmid DNA subjected to PCR amplification. The amount of DNA in each sample is proportional to the band intensity when run on a gel if low cycle number (<25 cycles) PCR is used ( 31 ), i.e. in the linear amplification range. Two of the most active oligonucleotides (ds S-X and unl CTTG-X) were tested. PCR analysis of transfected samples showed that the amounts of amplification product of all transfections were similar (Fig. 5 , lanes 2-4), indicating that the oligonucleotides had no effect on transfection efficiency. Negative control lanes included mock-transfected cells (Fig. 5 , lane 1) and a water blank (Fig. 5 , lane 6). In addition to transfected pRFX1VP16, another positive control included 2 ng pRFX1VP16 as template (Fig. 5 , lane 5).


Figure 5 . PCR. Lanes contain PCR-amplified DNA from: lane 1, cells alone (mock transfection); lane 2, cells transfected with plasmids pRFX1VP16 and p4XBCAT (p); lane 3, cells transfected with p and ds S-X; lane 4, cells transfected with p and unl CTTG-X; lane 5, 2 ng pRFX1VP16; lane 6, blank (water). Lane 7 contains molecular weight markers.

Levels of mRNA were decreased by the addition of active oligonucleotides/dumbbells

To determine if active oligonucleotides/dumbbells were effecting general transcription of the reporter plasmid, mRNA transcripts were measured using an RNase protection assay. Transfection of plasmids/oligonucleotides into Cos7 cells was performed as described and RNA was extracted. RNase assays revealed a decrease in CAT mRNA (transcribed by polymerase II) upon the addition of 50 nM core X-box oligonucleotides, (Fig. 6 , top panel; compare lane 1, no oligonucleotide added, to lanes 2-5). The ds S-X oligonucleotide (Fig. 6 , top panel, lane 2) yielded the largest decrease in mRNA levels. The protected band(s) is the predicted size (111 bp). In contrast, levels of 18S RNA (transcribed by polymerase I) were not altered by the addition of oligonucleotides (Fig. 6 , bottom panel, lanes 2-5; CAT RNA and 18S RNA were probed separately). In addition, levels of total RNA were not decreased by active oligonucleotides using a total RNA accumulation assay (data not shown).


Figure 6 . RNase protection assay. RNA harvested from cells transfected with: lane 1, plasmids pRFX1VP16 and p4XBCAT (p); lane 2, p + ds S-X; lane 3, p + ds X; lane 4, p + unl X; lane 5, p + unl CTTG-X; all probed with the CAT probe (top panel) or the 18S RNA probe (bottom panel). Lane 6, RNA from cells transfected with p, probed with tRNA (control). Lane 7, 173 nt probe alone; lane 8, DNA molecular weight marker. The presence of two bands in this gel is most likely due to RNA:DNA hybrid formation, which is also resistant to RNase. This will often arise when RNA from transient transfections is used (and hence contaminating DNA is present) (31). The protected 80 bp fragment of 18S RNA should normally appear as two closely migrating bands `due to a portion of the antisense probe rehybridizing to its complementary sequence', according to the manufacturer (Ambion).

DISCUSSION

In EMSAs using Raji nuclear extracts and a labeled X-box oligonucleotide probe, competitor oligonucleotides with the core X-box sequence were able to compete efficiently for complex formation. However, in direct binding assays, only the X dumbbell was able to form a detectable complex with an X-box protein identified as RFX1 under these conditions. Unligated irrelevant sequence oligonucleotides did not compete in vitro , but had activity in three different in vivo reporter gene assays. This suggested that the oligonucleotides inhibited transcription in a manner not predicted, i.e. not by competition with the reporter plasmid target for RFX1 binding. The PCR-based assay indicated that the oligonucleotides were not directly interfering with plasmid transfection. RNase protection assay analysis indicated that the oligonucleotides were inhibiting RNA polymerase II transcription in general.

Toxicity or cell viability is an important factor that should be considered when interpreting results. In the typical reporter gene assays used for assessing oligonucleotide activity, cell death can inadvertently contribute to `activity', since activity is commonly measured by decreases in reporter gene protein. While others have reported the sequence-specific blockage of transcription factors with oligonucleotide doses ranging from 10 nM to 7.5 [mu]M, no mention of cell viability/toxicity is made in some of the studies ( 3 , 5 ). Some of our earlier studies indicated that certain oligonucleotides were more toxic than others, usually when in the micromolar range (data not shown). There have been several reports of toxicity of phosphorothioates ( 32 , 33 ), however, in our studies, the ds S-X phosphorothioate (and another phosphorothioate with the same internal sequence as unl ctrl 3) was never toxic (as measured by cell viability) at the concentrations we tested (up to 5 [mu]M).

Factoring out toxicity, in our reporter gene assays all core X-box oligonucleotides were able to block RFX1VP16 activation of 4XBCAT. Interestingly, activity correlated with predicted oligonucleotide stability (i.e. the more stable the oligonucleotide, the more potent it was). Phosphorothioates would be expected to be the most stable due to their nuclease resistance in cells ( 34 ). Chu ( 9 ) reported the following order of stability (in human sera): dumbbells > hairpins > double strands > single strands, due to active single-strand endonucleases and less rapidly acting double-strand exonucleases. Thermodynamically, among the unligated dumbbells the expected order of stability is CTTG loop > T loop > A loop, based on DNA hairpin studies ( 11 ). Therefore, in terms of resistance to exonucleases and thermodynamic stability, the expected order of overall stability (and coincidently, the order of activity) for our oligonucleotides was ds S-X > unl CTTG-X > unl X > unl A-X > hairpin X > ds X. The melting temperature of unl X under highly denaturing conditions was 42.5oC, therefore, under physiological conditions unligated dumbbells would be expected to exist as stable duplex molecules. Even with a nick in the dumbbell (i.e. the unligated state), endonuclease degradation in this cell line could be minimal, allowing the oligonucleotides ample time to exert their effects. The stability of unligated dumbbells (and phosphorothioate oligonucleotides) may contribute to their apparent activity.

In summary, factors that may influence the success of DNA decoys or dumbbells include: the dose and toxicity profile of the oligonucleotide; the cell line; the affinity and specificity of the transcription factor for the decoy in vivo ; the affinity of the oligonucleotide toward transcriptional machinery; other non-specific effects. The study of DNA dumbbells presents a unique opportunity to test the effects of the addition of short, unmodified or `naturally occurring' phosphodiester oligonucleotide duplexes to cell systems. These dumbbells may have non-sequence-specific effects on the intracellular milieu, including inhibition of RNA polymerase II transcription. Hence dumbbells may prove to be useful tools for studies involving polymerase II transcription and gene expression. Interestingly, unligated dumbbells (referred to as `nicked' dumbbells) with phosphorothioate substitutions in the loops were recently found to have anti-HIV activity in a human T cell line ( 35 ). Unligated (nicked) dumbbells represent a new class of biologically active oligonucleotides with activities yet to be discovered.

ACKNOWLEDGEMENTS

C.S.Lim was supported in part by a NIH Pharmaceutical Chemistry Training Grant. The authors would like to thank Yoko S.Haga for T m data and Thomas E.Cheatham for helpful discussions.

REFERENCES

1 Hélène,C. and Toulme,J.J. (1990) Biochim. Biophys. Acta, 1049, 99-125.

2 Hélène,C. (1991) Anticancer Drug Des., 6, 569-584.

3 Bielinska,A., Shivdasani,R.A., Zhang,L.Q. and Nabel,G.J. (1990) Science, 250, 997-1000. MEDLINE Abstract

4 Holt,J.T. (1991) Antisense Res. Dev., 1, 365-369. MEDLINE Abstract

5 Clusel,C., Ugarte,E., Enjolras,N., Vasseur,M. and Blumenfeld,M. (1993) Nucleic Acids Res., 21, 3405-3411. MEDLINE Abstract

6 Cereghini,S., Blumenfeld,M. and Yaniv,M. (1988) Genes Dev., 2, 957-974. MEDLINE Abstract

7 Tanaka,H., Vickart,P., Bertrand,J.R., Rayner,B., Morvan,F., Imbach,J.L., Paulin,D. and Malvy,C. (1994) Nucleic Acids Res., 22, 3069-3074. MEDLINE Abstract

8 Brown,D.A., Kang,S.H., Gryaznov,S.M., DeDionisio,L., Heidenreich,O., Sullivan,S., Xu,X. and Nerenberg,M.I. (1994) J. Biol. Chem., 269, 26801-26805.

9 Chu,B.C. and Orgel,L.E. (1992) Nucleic Acids Res., 20, 5857-5858. MEDLINE Abstract

10 Wemmer,D. and Benight,A. (1985) Nucleic Acids Res., 13, 8611-8621. MEDLINE Abstract

11 Antao,V.P., Lai,S.Y. and Tinoco,I.J. (1991) Nucleic Acids Res., 19, 5901-5905. MEDLINE Abstract

12 Erie,D.A., Jones,R.A., Olson,W.K., Sinha,N.K. and Breslauer,K.J. (1989) Biochemistry, 28, 268-273. MEDLINE Abstract

13 Blommers,M.J., Walters,J.A., Haasnoot,C.A., Aelen,J.M., van der Marel,G.A., van Boom,J.H. and Hilbers,C.W. (1989) Biochemistry, 28, 7491-7498. MEDLINE Abstract

14 Senior,M.M., Jones,R.A. and Breslauer,K.J. (1988) Proc. Natl. Acad. Sci. USA, 85, 6242-6246. MEDLINE Abstract

15 Steimle,V., Durand,B., Barras,E., Zufferey,M., Hadam,M.R., Mach,B. and Reith,W. (1995) Genes Dev., 9, 1021-1032. MEDLINE Abstract

16 Lim,C.S. and Hunt,C.A. (1997) Nucleosides Nucleotides, in press.

17 Lim,C.S. and Hunt,C.A. (1994) BioTechniques, 17, 626-628. MEDLINE Abstract

18 Osborn,L., Kunkel,S. and Nabel,G.J. (1989) Proc. Natl. Acad. Sci. USA, 86, 2336-2340. MEDLINE Abstract

19 Zhang,X.Y., Jabrane-Ferrat,N., Asiedu,C.K., Samac,S., Peterlin,B.M. and Ehrlich,M. (1993) Mol. Cell. Biol., 13, 6810-6818. MEDLINE Abstract

20 Reith,W., Barras,E., Satola,S., Kobr,M., Reinhart,D., Sanchez,C.H. and Mach,B. (1989) Proc, Natl, Acad, Sci, USA, 86, 4200-4204.

21 Voliva,C.F., Jabrane-Ferrat,N. and Peterlin,B.M. (1996) Immunogenetics, 43, 20-26. MEDLINE Abstract

22 Neumann,J.R., Morency,C.A. and Russian,K.O. (1987) BioTechniques, 5, 444-447.

23 Voliva,C.F., Aronheim,A., Walker,M.D. and Peterlin,B.M. (1992) Mol. Cell. Biol., 12, 2383-2390. MEDLINE Abstract

24 Teramoto,N., Tonoyama,Y., Akagi,T., Sarker,A.B., Yoshino,T., Yamadori,I. and Takahashi,K. (1994) Acta Med. Okayama, 48, 189-193. MEDLINE Abstract

25 Kao,S.Y., Calman,A.F., Luciw,P.A. and Peterlin,B.M. (1987) Nature, 330, 489-493. MEDLINE Abstract

26 Teasdale,R.M., Matson,S.J., Fisher,E. and Krieg,A.M. (1994) Antisense Res. Dev., 4, 295-297. MEDLINE Abstract

27 Siegrist,C.A., Durand,B., Emery,P., David,E., Hearing,P., Mach,B. and Reith,W. (1993) Mol. Cell. Biol., 13, 6375-6384. MEDLINE Abstract

28 Reith,W., Ucla,C., Barras,E., Gaud,A., Durand,B., Herrero,S.C., Kobr,M. and Mach,B. (1994) Mol. Cell. Biol., 14, 1230-1244. MEDLINE Abstract

29 Antao,V.P. and Tinoco,I.J. (1992) Nucleic Acids Res., 20, 819-824. MEDLINE Abstract

30 Promega technical bulletin

31 Mason,P.J., Enver,T., Wilkinson,D. and Williams,J.G. (1993) In Hames,B.D. and Higgins,S.J. (eds), Gene Transcription: A Practical Approach. Oxford University Press, Oxford, UK, pp. 5-63.

32 Crooke,R.M. (1991) Anticancer Drug Des., 6, 609-646. MEDLINE Abstract

33 Chavany,C., Connell,Y. and Neckers,L. (1995) Mol. Pharmacol., 48, 738-746. MEDLINE Abstract

34 Uhlmann,E. and Peyman,A. (1990) Chem. Rev., 90, 543-584.

35 Yamakawa,H., Hosono,K., Ishibashi,T., Nakashima,H., Inagawa,T., Yamamoto,N., Takai,K. and Takaku,H. (1996) Nucleosides Nucleotides, 15, 519-529.


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*To whom correspondence should be addressed at present address: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA. Tel: +1 301 496 7443; Fax: +1 301 496 4951; Email: limc@dce41.nci.nih.gov
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